Bottom mount. It's much more stable than top mounting. Also, a joystick CAN be mounted too high. The standard for happ super and competition sticks is 1/2"-5/8" from the TOP of the joystick base to the top of the control panel. What this means:
Say you're using 3/4" MDF for your control panel; you want your stick depth to be 5/8". You'd have to rout away 1/4" of material from the bottom creating the recess. Like this:


You'd then mount the stick like so:

Look at how the stick is mounted. Small machine nuts and bolts. Not coming loose anytime soon. Very sturdy and the height is perfect. --->


FYI, the height is about 1/8" lower than an x-arcade stick. I designed it this way because as the pivot lowers, there is less movement necessary to activate the switches. Basically it's a bit more responsive than a flush mount. I also like doing it this way because it avoids the need for visible mounting bolts on the top of the cp.
EDIT:
Oops...I was a bit late on this one....
Helpful info either way...